Algorithmic Pot Generation: Algorithms for the Flexible-Tile Model of DNA Self-Assembly

TL;DR

This paper introduces algorithmic methods, including integer programming, for designing DNA nanostructures using a flexible-tile model, optimizing the assembly of complex target structures.

Contribution

It presents novel algorithmic solutions for selecting DNA components to efficiently assemble specified nanostructures within a flexible-tile framework.

Findings

Developed integer programming algorithms for DNA nanostructure design

Achieved optimal component selection for target structures

Enhanced understanding of DNA self-assembly algorithms

Abstract

Recent advancements in microbiology have motivated the study of the production of nanostructures with applications such as biomedical computing and molecular robotics. One way to construct these structures is to construct branched DNA molecules that bond to each other at complementary cohesive ends. One practical question is: given a target nanostructure, what is the optimal set of DNA molecules that assemble such a structure? We use a flexible-tile graph theoretic model to develop several algorithmic approaches, including a integer programming approach. These approaches take a target undirected graph as an input and output an optimal collection of component building blocks to construct the desired structure.